Figure 1 (Top) Diagram of an influenza A virus (FLUA) virion in section. The indicated glycoproteins embedded in the lipid membrane are the trimeric hemagglutinin (HA), which predominates, and the tetrameric neuraminidase (NA). The envelope also contains a small number of M2 ion channel proteins. The internal components are the M1 (matrix) protein and the viral ribonucleoprotein (RNP) consisting of RNA segments, associated nucleocapsid protein (NP), and the PA, PB1 and PB2 polymerase proteins. NS2 (NEP), also a virion protein, is not shown. (Bottom) Frozen-hydrated images of a spherical A/Aichi/2/68 X-31 virion (left) and a filamentous A/Udorn/72 virion (right)
(image courtesy of Peter Rosenthal, NIMR, London).
Figure 2 Orthomyxovirus genome organization. The genomic organization and ORFs are shown for genes that encode multiple proteins. Segments encoding the polymerase, hemagglutinin and nucleoprotein genes are not depicted as each encodes a single protein. (A) Influenza A virus PB1 segment ORFs. Initiation of PB1 translation is thought to be relatively inefficient based on Kozak’s rule, likely allowing initiation of PB1-F2 translation by ribosomal scanning and results in PB1-F2 proteins of different size. In addition, the use of a second AUG, present in many but not all viruses, in frame in the PB1 ORF as the initiation codon encodes the polypeptide PB1 N40, the C terminal 718 amino acids of PB1. (B) Influenza A virus segment 7 showing M1 and M2 mRNAs and their coding regions. M1 and M2 share 9 amino-terminal residues, including the initiating methionine; however, the ORF of M2 mRNA (nt 740–1004) differs from that of M1. (C) Influenza A virus segment 8 showing NS1 and NS2 (NEP) mRNAs and their coding regions. NS1 and NS2 (NEP) share 10 amino-terminal residues, including the initiating methionine. The ORF of NS2 (NEP) mRNA (nt 529-861) differs from that of NS1. (D) ORFs in Influenza B virus RNA segment 6, illustrating the overlapping reading frames of NB and NA. Nucleotide sequence surrounding the 2 AUG initiation codons, in the mRNA sense, is shown. (E) Influenza B virus RNA segment 7 ORFs and the organization of the ORFs used to translate the M1 and BM2 proteins. A stop–start pentanucleotide, thought to couple translation between the two ORFs, is illustrated. (F) Influenza C virus mRNAs derived from RNA segment 6. The unspliced and spliced mRNAs encode P42 and M1, respectively. The cleavage of P42 by a signal peptidase produces M1’(p31) and CM2. (G) Thogoto virus segment 6 showing M and ML. M is translated from a spliced mRNA with a stop codon that is generated by the splicing process itself, as in Influenza C virus M1 mRNA. ML is translated from the unspliced transcript and represents an elongated form of M with a C-terminal extension of 38 aa. (H) Isavirus mRNAs derived from segment 7. The unspliced mRNA encodes the NS protein and the spliced mRNA encodes a polypeptide of unknown function. (I) Isavirus mRNAs derived from segment 8. ORF1 starts at nucleotide 22 and encodes the M1 protein, ORF2 starts at nucleotide 36, in the+2 reading frame relative to ORF1 and encodes a polypeptide of unknown function. For all panels, the boxes represent different coding regions. Introns in the mRNAs are shown by the V-shaped lines; filled rectangles at the 5′ ends of mRNAs represent heterogeneous nucleotides derived from cellular RNAs that are covalently linked to viral sequences. Lines at the 5′ and 3′ termini of the mRNAs represent untranslated regions.
(Modified from Lamb and Horvath (1991). Trends Genet., 7, 261-266 and Garcia-Rosado et al. (2008). Virus Res., 133, 228-238.)
Figure 3 Phylogenetic relationships within the family Orthomyxoviridae. Nucleotide sequences of the polymerase basic 1 proteins (PB1) were aligned using transAlign and CLUSTAL W, and their phylogenetic relationships were determined by the neighbor-joining method (HKY model) using PAUP* (version 4.0b). The tree was mid-point rooted and bootstrap values (1000 replicates) are indicated on the branches. The GenBank accession numbers for the sequences used for comparison were (top to bottom) AF404346, GU830904, FJ861695, FJ861697, AF004985, M65866, M28060, AF170575, CY018763, CY018771, GU053121, CY044267 and FJ966080.